Tips & Hints
show them how to use UT Webspacehttps://webspace.utexas.edu/xythoswfs/. Timestamp for Microsoft Word documents: ALT + i together, release and hit T Date Stamp for Excel: CTRL + ; Time Stamp for Excel: CTRL + SHFT + :
NOTE: each pair will pick just one (1) pellet to purify. The other one should just be kept frozen as backup.
- each person should still make their own samples 1,2,3,4,5,6 for the Gel Though
Also, if they use Cyanase - they only need 1 ul of it since the stock concentration is greater than that of benzonase.
COMMON COMMENTS - Beer's Law
Correct images
show calculations
which spec did you use?
enough procedures but not onerous detail that is redundant to lab 1
analysis-error
conclusion-recap
future directions
GRAPHS: 1. max wavelength 2. all readings 3. table with data 4.graph with linear regression
hypothesis: does it hold for all concentrations?
Should mention creating linear best fit line in Excel (don't need to talk about other aspects of Excel since they have already used it)
When they work in pairs - have them start out on the 'expensive' stuff first. That way if they have to finish the lab another day and end up both doing the materials separately - we won't have made too much stuff.
'Expensive' stuff:
0.100 L LB broth (autoclaved) 200 ml 0.1M Tris base or Trizma base pH 7.5 using conc. HCl (hydrochloric acid) 1 ml 50 mg/ml Amp (filter sterilized)
50 ml 1 M Imidazole (filter-sterilized)
50 ml 10x PBS (Phosphate Buffered Saline, filter-sterilized)
'Cheap' stuff:
50 ml 5 N NaOH (Sodium Hydroxide) 100 ml 5x Tris-Glycine-SDS buffer 10 ml of 30% EtOH (ethanol) in autoclaved water
Enzyme Assay Lab
Lab Handout:
Teaching Points:
They can use multiple cuvettes to do their readings faster (i.e. have 9 or 10 of the same cuvettes instead of washing one multiple times)
Make them save their spectrophotometer file – NameEnzymeAssayDATE
Make them save their spectrophotometer file – NameEnzymeAssayDATE
Make them save their spectrophotometer file – NameEnzymeAssayDATE
MAKE sure they clean up afterwards before you sign them out.
Tips & Hints
they need to have all 3 titrations on the same graph in the end - to do so, they will need to creat 3 calculated volume columns and give them each a different name (e.g. CV1, CV2, and CV3).
Tips & Hints
show them how to use UT Webspacehttps://webspace.utexas.edu/xythoswfs/. to save their Image (.png) and Session (.pse) files. The first time they use it the have to 'sign up' on the Sign Up page.
Also there is an 'Advanced Upload' button that lets them have a drag and drop folder instead of uploading each file individually. (Much faster).
Beer's Law
Lab Handout:
Teaching Points:
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not Found
Tips & Hints
warm up specs for about 10 minutes before use
Henry spec reads very high on the Absorbance values - need to make sure they don't record their data if it is saturating the dector (>1.5 or 2 on the absorbance units)
Students should empty their cuvettes between EACH reading (i.e. for n=3 replicates, they shoudl empty the cuvette 3 times).
This takes longer but reinforces that just hitting the COLLECT button 3 times on the exact same sample does not constitute a true replicate.
To speed things up - they can get 3 cuvettes at a time and fill with a given dilution (Dil1, Dil2, Dil3, etc.)
-- then measure 3 in a row quickly.
They don't have to measure Dilution 1 - IF they know it is going to be above 1.5 Absorbance units.
Teaching Points For VDS Spring 2013 Labs
Tips & Hints
show them how to use UT Webspacehttps://webspace.utexas.edu/xythoswfs/.
Timestamp for Microsoft Word documents: ALT + i together, release and hit T
Date Stamp for Excel: CTRL + ;
Time Stamp for Excel: CTRL + SHFT + :
Beta-lactamase docking (a.k.a. VS4)
Lab Handout:Target Discovery
Lab Handout:ProtocolTargetDiscoveryVDS_Spring13.docx
VS3 lab
Lab Handout:LabVirtualScreen3_Phosphatase_VDS_Spring13.docx
Teaching Points:
TeachingPointsMentors_VS3.docx
Protein Characterization Lab
Lab Handout:LabProteinCharacterizationVDS_Spring13.doc
SDS-PAGE mini_PROTEAN setup.pdf
Teaching Points:
TeachingPointsMentors_CharacterizationLab.docx
Virtual Screening 2
Lab Handout:LabVirtualScreen2VDS_Spring13.doc
Teaching Points:
TeachingPointsMentors_VS2lab.docx
Protein Purification Lab
NOTE: each pair will pick just one (1) pellet to purify. The other one should just be kept frozen as backup.- each person should still make their own samples 1,2,3,4,5,6 for the Gel Though
Also, if they use Cyanase - they only need 1 ul of it since the stock concentration is greater than that of benzonase.
Lab Handout:
LabProteinPurificationVDS_Spring13.docx
Teaching Points:
TeachingPointsMentors_PurificationLab.docx
Virtual Screening 1
Lab Handout:LabVirtualScreen1VDS_Spring13.docx
16dhfr-ligsX.sdf
BasicLinux.pdf
The other files for docking are on the DDFE in /home/chem204/LabVirtualScreening1files
Teaching Points: (password protected)
TeachingPointsMentors_VS1lab.docx
Protein Expression
Lab Handout:LabProteinExpressionVDS_Spring13.docx
Teaching Points:
TeachingPointsMentors_ExpressionLab.docx
PyMol 3
Lab Handout:LabPyMol3_VDS_Spring13.doc
DHFR-hs.pdb
dhfr-lc.pdb
Teaching Points:
TeachingPointsMentors_PyMol3_Sp13.docx
Buffer Titration
Lab Handout:LabBufferTitrationVDS_Spring13.doc
Teaching Points:
TeachingPointsMentors_BufferTitration.docx
H-H Exercise Answers: (password protected)
CLASS HANDOUT SOLUTIONS:
VDS_6thClassJTB_Spring12Henderson-HasselbalchExercisesForSTAFF.docx
LAB HANDOUT SOLUTION - this is VERSION 2 - so, I know its right.....?
H-HeqnAnswerforBufferTitrationLabHandoutPsswd.docx
PyMol 2
Lab Handout:LabPyMol2_VDS_Spring12.doc
Teaching Points:
TeachingPointsMentors_PyMol2.docx
COMMON COMMENTS - PyMol2
Beer's Law
Lab Handout:LabBeer'sLawVDS_Spring13.doc
Teaching Points:
TeachingPointsMentors_BeersLaw.docx
ExampleBeersLawScreeShot020613.JPG
COMMON COMMENTS - Beer's Law
Correct images
show calculations
which spec did you use?
enough procedures but not onerous detail that is redundant to lab 1
analysis-error
conclusion-recap
future directions
GRAPHS: 1. max wavelength 2. all readings 3. table with data 4.graph with linear regression
hypothesis: does it hold for all concentrations?
Should mention creating linear best fit line in Excel (don't need to talk about other aspects of Excel since they have already used it)
LAST WEEK:
Lit Search & Endnote Web
BibliographyEndNoteExerciseVDS_Spring13.docLiteratureAssignment_VDSSpring2013.docx
LITERATURE_EndNote_LitAnswersCOMBINEDforMentors_OLD2012version.docx
this last one is password protected with Mentor password
Buffers & Solutions Lab:
Lab Handout:LabBuffersandSolutionsVDS_Spring13.docx
NOTE: the LB amount is WRONG on the handout - they should only make 100ml of LB.
Teaching Points:
TeachingPointsMentors_BuffersAndSolutions.docx
When they work in pairs - have them start out on the 'expensive' stuff first. That way if they have to finish the lab another day and end up both doing the materials separately - we won't have made too much stuff.
'Expensive' stuff:
0.100 L LB broth (autoclaved)200 ml 0.1M Tris base or Trizma base pH 7.5 using conc. HCl (hydrochloric acid)
1 ml 50 mg/ml Amp (filter sterilized)
50 ml 1 M Imidazole (filter-sterilized)
50 ml 10x PBS (Phosphate Buffered Saline, filter-sterilized)
'Cheap' stuff:
50 ml 5 N NaOH (Sodium Hydroxide)100 ml 5x Tris-Glycine-SDS buffer
10 ml of 30% EtOH (ethanol) in autoclaved water
Enzyme Assay Lab
Lab Handout:Teaching Points:
They can use multiple cuvettes to do their readings faster (i.e. have 9 or 10 of the same cuvettes instead of washing one multiple times)
Make them save their spectrophotometer file – NameEnzymeAssayDATE
Make them save their spectrophotometer file – NameEnzymeAssayDATE
Make them save their spectrophotometer file – NameEnzymeAssayDATE
MAKE sure they clean up afterwards before you sign them out.
Buffer Titration
Lab Handout:Teaching Points:
Henderson-Hasselbalch exercise answer sheet (password protected).VDS_6thClassJTB_Spring12Henderson-HasselbalchExercisesForSTAFF.docx
Tips & Hints
they need to have all 3 titrations on the same graph in the end - to do so, they will need to creat 3 calculated volume columns and give them each a different name (e.g. CV1, CV2, and CV3).
PyMol2
Lab Handout:Teaching Points:
DHFR-hs.pdb
Helix.pdb
Tips & Hints
show them how to use UT Webspacehttps://webspace.utexas.edu/xythoswfs/. to save their Image (.png) and Session (.pse) files. The first time they use it the have to 'sign up' on the Sign Up page.
Also there is an 'Advanced Upload' button that lets them have a drag and drop folder instead of uploading each file individually. (Much faster).
Beer's Law
Lab Handout:Teaching Points:
[[image:/i/file_not_found.png width="32" height="32" caption="File Not Found"]]File Not Found
Tips & Hints
warm up specs for about 10 minutes before use
Henry spec reads very high on the Absorbance values - need to make sure they don't record their data if it is saturating the dector (>1.5 or 2 on the absorbance units)
Students should empty their cuvettes between EACH reading (i.e. for n=3 replicates, they shoudl empty the cuvette 3 times).
This takes longer but reinforces that just hitting the COLLECT button 3 times on the exact same sample does not constitute a true replicate.
To speed things up - they can get 3 cuvettes at a time and fill with a given dilution (Dil1, Dil2, Dil3, etc.)
-- then measure 3 in a row quickly.
They don't have to measure Dilution 1 - IF they know it is going to be above 1.5 Absorbance units.